On my esy mk4 I dropped it out the bottom, but then I wanted to change the box at the same time.
Theres more space for it to go out the bottom. Then again, it seems a bit overkill if you're just changing the engine and you'd need to setup your gear selector doing it this way which can be a pain.
Also, if you drop it with the box attached you've got the extra work of puling out the driveshafts, which entails moving the hubs..etc.etc..